We utilize two stage procedure to fix it. First, we synchronize Alice and Bob's laser pulses with Charlie's clock [1]}, [2]}. Charlie sends two 250 MHz synchronized laser pulse trains to Alice and Bob through the synchronization fiber channel, respectively. The two laser trains are used to lock the local clock of the signal generators, which then generate signal pulses in both sides with a pulse duration of 280 ps. The measured arrival times in Charlie side are used for feedback signal to adjust the relative delay between Alice's and Bob's synchronization laser trains. With such an arrangement, the fluctuation of the arrival time decrease to  10 ps, negligible comparing to the signal pulse duration of 280 ps.
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